Research workbench

Concanavalin a complexed to methyl ALPHA1-2 mannobioside

Analyse Concanavalin a complexed to methyl ALPHA1-2 mannobioside in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BXH
Type: protein
Length: 948 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Concanavalin-a
UniProt: P02866
Ligands: AMG, MMA, MN, CA
Pockets: 6 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Concanavalin-a	protein	237	5% helix, 46% strand	P02866

Ligands and binding sites

AMG · methyl alpha-D-galactopyranoside · ligand · 3 copies · chains A, D
MMA · methyl alpha-D-mannopyranoside · sugar · 3 copies · chains A, B, C
MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1125	0.88	0.90	171	empty
2	166	0.47	0.76	22	empty
3	162	0.44	0.75	24	empty
4	61	0.36	0.78	21	empty
5	54	0.32	0.77	18	empty

Interfaces

6 interfaces between chains.

A–B · 1201 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1194 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 1134 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 1133 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1BXH · Concanavalin a complexed to methyl ALPHA1-2 mannobioside · the same entry in another collection · chain A against A, TM-score 1.00
P02866 · AlphaFold monomer V2.0 prediction for concanavalin-a (P02866) · a predicted model of the same protein · chain A against A, TM-score 0.50

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P02866
Elsewhere: RCSB PDB 1BXH · PDBe 1BXH · UniProt P02866

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